Alignments for a candidate for leuC in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Pseudomonas stutzeri RCH2

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF2541 Psest_2591 3-isopropylmalate dehydratase, large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__psRCH2:GFF2541
          Length = 475

 Score =  607 bits (1564), Expect = e-178
 Identities = 308/470 (65%), Positives = 366/470 (77%), Gaps = 8/470 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+KL++ H V   ++ + L+YIDRH++HEVTSPQAF+GLR   R   +     AT D
Sbjct: 4   KTLYDKLWEMHEVKRRDDGSSLIYIDRHILHEVTSPQAFEGLRLANRKPWRIDANIATPD 63

Query: 63  HNVSTQTKDINACG------EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQG 116
           HNV T TK     G      E++RIQ+Q L +NC +FG+  + +N   QGIVHV+GPEQG
Sbjct: 64  HNVPT-TKGERQGGLEAIADEVSRIQVQTLDENCDDFGILEFKMNDVRQGIVHVIGPEQG 122

Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176
            TLPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L   + K M++ V+GK   
Sbjct: 123 ATLPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMQVRVEGKLPF 182

Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236
           G+TAKDIVLA+IGK G+AGG GH +EF G AIRDLSMEGRMT+CNM+IE GA+ G+VA D
Sbjct: 183 GVTAKDIVLAVIGKIGTAGGNGHALEFAGSAIRDLSMEGRMTICNMSIEAGARVGMVAVD 242

Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296
           E T  YV+GR  APKG D+D AV  W+ L +D+ A FDTVV L+AE+I PQV+WGT+P  
Sbjct: 243 EKTIAYVEGRPFAPKGDDWDKAVELWQGLVSDDDAVFDTVVELKAEDIKPQVSWGTSPEM 302

Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356
           V++V+  +PDPA  ADPV+R S  +AL YMGL    P+TE+ +D+VFIGSCTNSRIEDLR
Sbjct: 303 VLAVDQKVPDPAVEADPVKRDSIMRALKYMGLNANQPITEIKLDRVFIGSCTNSRIEDLR 362

Query: 357 AAAEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNN 415
           AAAE+AKGRKVA  V QALVVPGSG VK QAEAEGLDKIF+EAGFEWR PGCSMCLAMN 
Sbjct: 363 AAAEVAKGRKVAANVKQALVVPGSGLVKQQAEAEGLDKIFVEAGFEWREPGCSMCLAMNP 422

Query: 416 DRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           D+L  GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAVTGHF D+R +
Sbjct: 423 DKLGSGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVTGHFIDVREL 472


Lambda     K      H
   0.317    0.134    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 758
Number of extensions: 20
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 466
Length of database: 475
Length adjustment: 33
Effective length of query: 433
Effective length of database: 442
Effective search space:   191386
Effective search space used:   191386
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF2541 Psest_2591 (3-isopropylmalate dehydratase, large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00170.hmm
# target sequence database:        /tmp/gapView.24911.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.7e-239  781.1   1.3   2.1e-239  780.7   1.3    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2541  Psest_2591 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2541  Psest_2591 3-isopropylmalate dehydratase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  780.7   1.3  2.1e-239  2.1e-239       2     466 .]       3     472 ..       2     472 .. 0.98

  Alignments for each domain:
  == domain 1  score: 780.7 bits;  conditional E-value: 2.1e-239
                           TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr.....d 71 
                                          ktly+kl++ h vk+ +++++l+yidrh++hevtspqafeglr a+rk  r+d  +at dhn++t++       
  lcl|FitnessBrowser__psRCH2:GFF2541   3 GKTLYDKLWEMHEVKRRDDGSSLIYIDRHILHEVTSPQAFEGLRLANRKPWRIDANIATPDHNVPTTKGerqggL 77 
                                         59***************************************************************9876455543 PP

                           TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                           i +e++++qv++l++n+++fg+  f +++++qgivhv+gpe+g tlpg+t+vcgdsht+thgafgala gigt
  lcl|FitnessBrowser__psRCH2:GFF2541  78 EAIADEVSRIQVQTLDENCDDFGILEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGALAHGIGT 152
                                         46899********************************************************************** PP

                           TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcn 221
                                         sevehvlatq l+ ++ k+++++vegkl  g+takdi+la+igkig+agg g+ +efag airdlsme+rmt+cn
  lcl|FitnessBrowser__psRCH2:GFF2541 153 SEVEHVLATQCLVAKKMKNMQVRVEGKLPFGVTAKDIVLAVIGKIGTAGGNGHALEFAGSAIRDLSMEGRMTICN 227
                                         *************************************************************************** PP

                           TIGR00170 222 maieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgq 296
                                         m+ieaga+ g++a de t++yv +r++apkg++++kav+ w+ l +d++a+fd+vv l+a+di pqv+wgt+p++
  lcl|FitnessBrowser__psRCH2:GFF2541 228 MSIEAGARVGMVAVDEKTIAYVEGRPFAPKGDDWDKAVELWQGLVSDDDAVFDTVVELKAEDIKPQVSWGTSPEM 302
                                         *************************************************************************** PP

                           TIGR00170 297 vlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnv 371
                                         vl+v+++vpdp+  adpv++ s+ +al+y+gl++++++++ik+d+vfigsctnsriedlraaaev+kg+kva nv
  lcl|FitnessBrowser__psRCH2:GFF2541 303 VLAVDQKVPDPAVEADPVKRDSIMRALKYMGLNANQPITEIKLDRVFIGSCTNSRIEDLRAAAEVAKGRKVAANV 377
                                         *************************************************************************** PP

                           TIGR00170 372 klalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlv 446
                                         k+alvvpgsglvk+qae+egldkif+eagfewre+gcs+cl+mn+d+l+++e castsnrnfegrqg+g+rthlv
  lcl|FitnessBrowser__psRCH2:GFF2541 378 KQALVVPGSGLVKQQAEAEGLDKIFVEAGFEWREPGCSMCLAMNPDKLGSGEHCASTSNRNFEGRQGAGGRTHLV 452
                                         *************************************************************************** PP

                           TIGR00170 447 spamaaaaavagkfvdirel 466
                                         spamaaaaav+g+f+d+rel
  lcl|FitnessBrowser__psRCH2:GFF2541 453 SPAMAAAAAVTGHFIDVREL 472
                                         ******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (475 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.29
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis